TY - STD TI - Vera Opatova, Chris A Hamilton, Marshal Hedin, Laura Montes De Oca, Jiři Král, Jason E Bond, Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data, Systematic Biology, syz064, https://doi.org/10.1093/sysbio/syz064. ID - ref1 ER - TY - STD TI - World Spider Catalog 2018. https://wsc.nmbe.ch/. Accessed on 5 Feb 2018. UR - https://wsc.nmbe.ch/ ID - ref2 ER - TY - JOUR AU - Main, B. Y. PY - 1978 DA - 1978// TI - Biology of the arid-adapted Australian trapdoor spider Anidiops villosus (rainbow) JO - Bull Br Arachnol Soc VL - 4 ID - Main1978 ER - TY - JOUR AU - Bond, J. E. AU - Hedin, M. C. AU - Ramirez, M. G. AU - Opell, B. D. PY - 2001 DA - 2001// TI - Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus JO - Mol Ecol VL - 10 UR - https://doi.org/10.1046/j.1365-294X.2001.01233.x DO - 10.1046/j.1365-294X.2001.01233.x ID - Bond2001 ER - TY - JOUR AU - Sanggaard, K. W. AU - Bechsgaard, J. S. AU - Fang, X. AU - Duan, J. AU - Dyrlund, T. F. AU - Gupta, V. AU - Jiang, X. AU - Cheng, L. AU - Fan, D. AU - Feng, Y. AU - Han, L. PY - 2014 DA - 2014// TI - Spider genomes provide insight into composition and evolution of venom and silk JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms4765 DO - 10.1038/ncomms4765 ID - Sanggaard2014 ER - TY - JOUR AU - Hamilton, C. A. AU - Lemmon, A. R. AU - Lemmon, E. M. AU - Bond, J. E. PY - 2016 DA - 2016// TI - Expanding anchored hybrid enrichment to resolve both deep and shallow relationships within the spider tree of life JO - BMC Evol Biol VL - 16 UR - https://doi.org/10.1186/s12862-016-0769-y DO - 10.1186/s12862-016-0769-y ID - Hamilton2016 ER - TY - JOUR AU - Mason, L. D. AU - Tomlinson, S. AU - Withers, P. C. AU - Main, B. Y. PY - 2013 DA - 2013// TI - Thermal and hygric physiology of Australian burrowing mygalomorph spiders (Aganippe spp.) JO - J Comp Physiol B VL - 183 UR - https://doi.org/10.1007/s00360-012-0681-8 DO - 10.1007/s00360-012-0681-8 ID - Mason2013 ER - TY - JOUR AU - Criscuolo, F. AU - Font-Sala, C. AU - Bouillaud, F. AU - Poulin, N. AU - Trabalon, M. PY - 2010 DA - 2010// TI - Increased ROS production: a component of the longevity equation in the male mygalomorph, Brachypelma albopilosa JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0013104 DO - 10.1371/journal.pone.0013104 ID - Criscuolo2010 ER - TY - JOUR AU - Diego-García, E. AU - Peigneur, S. AU - Clynen, E. AU - Marien, T. AU - Czech, L. AU - Schoofs, L. AU - Tytgat, J. PY - 2012 DA - 2012// TI - Molecular diversity of the telson and venom components from Pandinus cavimanus (Scorpionidae Latreille 1802): transcriptome, venomics and function JO - Proteomics. VL - 12 UR - https://doi.org/10.1002/pmic.201100409 DO - 10.1002/pmic.201100409 ID - Diego-García2012 ER - TY - JOUR AU - Pérez-Miles, F. AU - Guadanucci, J. P. AU - Jurgilas, J. P. AU - Becco, R. AU - Perafán, C. PY - 2017 DA - 2017// TI - Morphology and evolution of scopula, pseudoscopula and claw tufts in Mygalomorphae (Araneae) JO - Zoomorphology. VL - 136 UR - https://doi.org/10.1007/s00435-017-0364-9 DO - 10.1007/s00435-017-0364-9 ID - Pérez-Miles2017 ER - TY - JOUR AU - Gregory, T. R. AU - Shorthouse, D. P. PY - 2003 DA - 2003// TI - Genome sizes of spiders JO - J Hered VL - 94 UR - https://doi.org/10.1093/jhered/esg070 DO - 10.1093/jhered/esg070 ID - Gregory2003 ER - TY - STD TI - Genome List Genome NCBI. https://www.ncbi.nlm.nih.gov/genome/browse#!/eukaryotes/. Accessed on 5 Feb 2018. UR - https://www.ncbi.nlm.nih.gov/genome/browse#!/eukaryotes/ ID - ref12 ER - TY - JOUR AU - Yeates, D. K. AU - Meusemann, K. AU - Trautwein, M. AU - Wiegmann, B. AU - Zwick, A. PY - 2016 DA - 2016// TI - Power, resolution and bias: recent advances in insect phylogeny driven by the genomic revolution JO - Curr Opin Insect Sci VL - 13 UR - https://doi.org/10.1016/j.cois.2015.10.007 DO - 10.1016/j.cois.2015.10.007 ID - Yeates2016 ER - TY - JOUR AU - Garrison, N. L. AU - Rodriguez, J. AU - Agnarsson, I. AU - Coddington, J. A. AU - Griswold, C. E. AU - Hamilton, C. A. AU - Hedin, M. AU - Kocot, K. M. AU - Ledford, J. M. AU - Bond, J. E. PY - 2016 DA - 2016// TI - Spider phylogenomics: untangling the spider tree of life JO - PeerJ. VL - 4 UR - https://doi.org/10.7717/peerj.1719 DO - 10.7717/peerj.1719 ID - Garrison2016 ER - TY - JOUR AU - Wheeler, W. C. AU - Coddington, J. A. AU - Crowley, L. M. AU - Dimitrov, D. AU - Goloboff, P. A. AU - Griswold, C. E. AU - Hormiga, G. AU - Prendini, L. AU - Ramírez, M. J. AU - Sierwald, P. AU - Almeida-Silva, L. PY - 2017 DA - 2017// TI - The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling JO - Cladistics. VL - 33 UR - https://doi.org/10.1111/cla.12182 DO - 10.1111/cla.12182 ID - Wheeler2017 ER - TY - JOUR AU - Rodriguez, J. AU - Jones, T. H. AU - Sierwald, P. AU - Marek, P. E. AU - Shear, W. A. AU - Brewer, M. S. AU - Kocot, K. M. AU - Bond, J. E. PY - 2018 DA - 2018// TI - Step-wise evolution of complex chemical defenses in millipedes: a phylogenomic approach JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-19996-6 DO - 10.1038/s41598-018-19996-6 ID - Rodriguez2018 ER - TY - JOUR AU - Schwentner, M. AU - Combosch, D. J. AU - Nelson, J. P. AU - Giribet, G. PY - 2017 DA - 2017// TI - A phylogenomic solution to the origin of insects by resolving crustacean-hexapod relationships JO - Curr Biol VL - 27 UR - https://doi.org/10.1016/j.cub.2017.05.040 DO - 10.1016/j.cub.2017.05.040 ID - Schwentner2017 ER - TY - JOUR AU - Undheim, E. AU - Sunagar, K. AU - Herzig, V. AU - Kely, L. AU - Low, D. AU - Jackson, T. AU - Jones, A. AU - Kurniawan, N. AU - King, G. AU - Ali, S. AU - Antunes, A. PY - 2013 DA - 2013// TI - A proteomics and transcriptomics investigation of the venom from the barychelid spider Trittame loki (brush-foot trapdoor) JO - Toxins. VL - 5 UR - https://doi.org/10.3390/toxins5122488 DO - 10.3390/toxins5122488 ID - Undheim2013 ER - TY - JOUR AU - Frías-López, C. AU - Almeida, F. C. AU - Guirao-Rico, S. AU - Vizueta, J. AU - Sánchez-Gracia, A. AU - Arnedo, M. A. AU - Rozas, J. PY - 2015 DA - 2015// TI - Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae) JO - PeerJ. VL - 3 UR - https://doi.org/10.7717/peerj.1064 DO - 10.7717/peerj.1064 ID - Frías-López2015 ER - TY - JOUR AU - Leavitt, D. H. AU - Starrett, J. AU - Westphal, M. F. AU - Hedin, M. PY - 2015 DA - 2015// TI - Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae) JO - Mol Phylogenet Evol VL - 91 UR - https://doi.org/10.1016/j.ympev.2015.05.016 DO - 10.1016/j.ympev.2015.05.016 ID - Leavitt2015 ER - TY - JOUR AU - Hedin, M. AU - Derkarabetian, S. AU - Ramírez, M. J. AU - Vink, C. AU - Bond, J. E. PY - 2018 DA - 2018// TI - Phylogenomic reclassification of the world’s most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-19946-2 DO - 10.1038/s41598-018-19946-2 ID - Hedin2018 ER - TY - JOUR AU - Matz, M. V. PY - 2018 DA - 2018// TI - Fantastic beasts and how to sequence them: ecological genomics for obscure model organisms JO - Trends Genet VL - 34 UR - https://doi.org/10.1016/j.tig.2017.11.002 DO - 10.1016/j.tig.2017.11.002 ID - Matz2018 ER - TY - JOUR AU - Bond, J. E. PY - 2012 DA - 2012// TI - Phylogenetic treatment and taxonomic revision of the trapdoor spider genus Aptostichus Simon (Araneae, Mygalomorphae, Euctenizidae) JO - ZooKeys. VL - 252 UR - https://doi.org/10.3897/zookeys.252.3588 DO - 10.3897/zookeys.252.3588 ID - Bond2012 ER - TY - JOUR AU - Bond, J. E. AU - Stockman, A. K. PY - 2008 DA - 2008// TI - An integrative method for delimiting cohesion species: finding the population-species interface in a group of Californian trapdoor spiders with extreme genetic divergence and geographic structuring JO - Syst Biol VL - 57 UR - https://doi.org/10.1080/10635150802302443 DO - 10.1080/10635150802302443 ID - Bond2008 ER - TY - JOUR AU - Simão, F. A. AU - Waterhouse, R. M. AU - Ioannidis, P. AU - Kriventseva, E. V. AU - Zdobnov, E. M. PY - 2015 DA - 2015// TI - BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs JO - Bioinformatics. VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv351 DO - 10.1093/bioinformatics/btv351 ID - Simão2015 ER - TY - JOUR AU - Gurtan, A. M. AU - D’Andrea, A. D. PY - 2006 DA - 2006// TI - Dedicated to the core: understanding the Fanconi anemia complex JO - DNA Repair VL - 5 UR - https://doi.org/10.1016/j.dnarep.2006.05.009 DO - 10.1016/j.dnarep.2006.05.009 ID - Gurtan2006 ER - TY - JOUR AU - Howlett, N. G. AU - Taniguchi, T. AU - Olson, S. AU - Cox, B. AU - Waisfisz, Q. AU - Die-Smulders, C. AU - Persky, N. AU - Grompe, M. AU - Joenje, H. AU - Pals, G. AU - Ikeda, H. PY - 2002 DA - 2002// TI - Biallelic inactivation of BRCA2 in Fanconi anemia JO - Science. VL - 297 UR - https://doi.org/10.1126/science.1073834 DO - 10.1126/science.1073834 ID - Howlett2002 ER - TY - JOUR AU - Wang, A. T. AU - Smogorzewska, A. PY - 2015 DA - 2015// TI - SnapShot: Fanconi anemia and associated proteins JO - Cell. VL - 160 UR - https://doi.org/10.1016/j.cell.2014.12.031 DO - 10.1016/j.cell.2014.12.031 ID - Wang2015 ER - TY - JOUR AU - Hughes, A. L. AU - Friedman, R. PY - 2005 DA - 2005// TI - Loss of ancestral genes in the genomic evolution of Ciona intestinalis JO - Evol Dev VL - 7 UR - https://doi.org/10.1111/j.1525-142X.2005.05022.x DO - 10.1111/j.1525-142X.2005.05022.x ID - Hughes2005 ER - TY - JOUR AU - Stanley, E. C. AU - Azzinaro, P. A. AU - Vierra, D. A. AU - Howlett, N. G. AU - Irvine, S. Q. PY - 2016 DA - 2016// TI - The simple chordate Ciona intestinalis has a reduced complement of genes associated with Fanconi anemia JO - Evol Bioinforma VL - 12 UR - https://doi.org/10.4137/EBO.S37920 DO - 10.4137/EBO.S37920 ID - Stanley2016 ER - TY - JOUR AU - Herzig, V. AU - Wood, D. L. AU - Newell, F. AU - Chaumeil, P. A. AU - Kaas, Q. AU - Binford, G. J. AU - Nicholson, G. M. AU - Gorse, D. AU - King, G. F. PY - 2010 DA - 2010// TI - ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures JO - Nucleic Acids Res VL - 39 ID - Herzig2010 ER - TY - JOUR AU - Rice, P. PY - 2000 DA - 2000// TI - Longden I Bleasby A. EMBOSS: The european molecular biology open software suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - JOUR AU - King, G. F. AU - Hardy, M. C. PY - 2013 DA - 2013// TI - Spider-venom peptides: structure, pharmacology, and potential for control of insect pests JO - Annu Rev Entomol VL - 58 UR - https://doi.org/10.1146/annurev-ento-120811-153650 DO - 10.1146/annurev-ento-120811-153650 ID - King2013 ER - TY - JOUR AU - Bond, J. E. PY - 2004 DA - 2004// TI - Systematics of the Californian euctenizine spider genus Apomastus (Araneae: Mygalomorphae: Cyrtaucheniidae): the relationship between molecular and morphological taxonomy JO - Invertebr Syst VL - 18 UR - https://doi.org/10.1071/IS04008 DO - 10.1071/IS04008 ID - Bond2004 ER - TY - JOUR AU - Saez, N. J. AU - Senff, S. AU - Jensen, J. E. AU - Er, S. Y. AU - Herzig, V. AU - Rash, L. D. AU - King, G. F. PY - 2010 DA - 2010// TI - Spider-venom peptides as therapeutics JO - Toxins. VL - 2 UR - https://doi.org/10.3390/toxins2122851 DO - 10.3390/toxins2122851 ID - Saez2010 ER - TY - STD TI - Maun A, Maun MA. The biology of coastal sand dunes. Oxford: Oxford University Press; 2009. ID - ref36 ER - TY - JOUR AU - Ryberg, W. A. AU - Fitzgerald, L. A. PY - 2015 DA - 2015// TI - Sand grain size composition influences subsurface oxygen diffusion and distribution of an endemic, psammophilic lizard JO - J Zool VL - 295 UR - https://doi.org/10.1111/jzo.12184 DO - 10.1111/jzo.12184 ID - Ryberg2015 ER - TY - JOUR AU - McLachlan, A. PY - 1991 DA - 1991// TI - Ecology of coastal dune fauna JO - J Arid Environ VL - 21 UR - https://doi.org/10.1016/S0140-1963(18)30684-0 DO - 10.1016/S0140-1963(18)30684-0 ID - McLachlan1991 ER - TY - JOUR AU - Longcore, T. PY - 2003 DA - 2003// TI - Terrestrial arthropods as indicators of ecological restoration success in coastal sage scrub (California, USA) JO - Restor Ecol VL - 11 UR - https://doi.org/10.1046/j.1526-100X.2003.rec0221.x DO - 10.1046/j.1526-100X.2003.rec0221.x ID - Longcore2003 ER - TY - JOUR AU - Bolger, A. M. AU - Lohse, M. AU - Usadel, B. PY - 2014 DA - 2014// TI - Trimmomatic: a flexible trimmer for Illumina sequence data JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu170 DO - 10.1093/bioinformatics/btu170 ID - Bolger2014 ER - TY - JOUR AU - Grabherr, M. G. AU - Haas, B. J. AU - Yassour, M. AU - Levin, J. Z. AU - Thompson, D. A. AU - Amit, I. AU - Adiconis, X. AU - Fan, L. AU - Raychowdhury, R. AU - Zeng, Q. AU - Chen, Z. PY - 2011 DA - 2011// TI - Full-length transcriptome assembly from RNA-Seq data without a reference genome JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1883 DO - 10.1038/nbt.1883 ID - Grabherr2011 ER - TY - JOUR AU - Haas, B. J. AU - Papanicolaou, A. AU - Yassour, M. AU - Grabherr, M. AU - Blood, P. D. AU - Bowden, J. AU - Couger, M. B. AU - Eccles, D. AU - Li, B. AU - Lieber, M. AU - MacManes, M. D. PY - 2013 DA - 2013// TI - De novo transcript sequence reconstruction from RNA-seq using the trinity platform for reference generation and analysis JO - Nat Protoc VL - 8 UR - https://doi.org/10.1038/nprot.2013.084 DO - 10.1038/nprot.2013.084 ID - Haas2013 ER - TY - JOUR AU - Li, B. AU - Dewey, C. N. PY - 2011 DA - 2011// TI - RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-323 DO - 10.1186/1471-2105-12-323 ID - Li2011 ER - TY - JOUR AU - Smith-Unna, R. AU - Boursnell, C. AU - Patro, R. AU - Hibberd, J. M. AU - Kelly, S. PY - 2016 DA - 2016// TI - TransRate: reference-free quality assessment of de novo transcriptome assemblies JO - Genome Res VL - 26 UR - https://doi.org/10.1101/gr.196469.115 DO - 10.1101/gr.196469.115 ID - Smith-Unna2016 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. AU - Marth, G. AU - Abecasis, G. AU - Durbin, R. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics. VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - STD TI - Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson D, Shenker S, Stoica I, Karp RM, Sittler T. Faster and more accurate sequence alignment with SNAP. arXiv preprint arXiv:1111.5572. 2011. ID - ref46 ER - TY - JOUR AU - Patro, R. AU - Duggal, G. AU - Love, M. I. AU - Irizarry, R. A. AU - Kingsford, C. PY - 2017 DA - 2017// TI - Salmon provides fast and bias-aware quantification of transcript expression JO - Nat Methods VL - 14 UR - https://doi.org/10.1038/nmeth.4197 DO - 10.1038/nmeth.4197 ID - Patro2017 ER - TY - JOUR AU - Waterhouse, R. M. AU - Seppey, M. AU - Simão, F. A. AU - Manni, M. AU - Ioannidis, P. AU - Klioutchnikov, G. AU - Kriventseva, E. V. AU - Zdobnov, E. M. PY - 2017 DA - 2017// TI - BUSCO applications from quality assessments to gene prediction and phylogenomics JO - Mol Biol Evol VL - 35 UR - https://doi.org/10.1093/molbev/msx319 DO - 10.1093/molbev/msx319 ID - Waterhouse2017 ER - TY - JOUR AU - Finn, R. D. AU - Clements, J. AU - Eddy, S. R. PY - 2011 DA - 2011// TI - HMMER web server: interactive sequence similarity searching JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr367 DO - 10.1093/nar/gkr367 ID - Finn2011 ER - TY - JOUR AU - Lafond-Lapalme, J. AU - Duceppe, M. O. AU - Wang, S. AU - Moffett, P. AU - Mimee, B. PY - 2017 DA - 2017// TI - A new method for decontamination of de novo transcriptomes using a hierarchical clustering algorithm JO - Bioinformatics. VL - 33 ID - Lafond-Lapalme2017 ER - TY - JOUR AU - Altschul, S. F. AU - Gish, W. AU - Miller, W. AU - Myers, E. W. AU - Lipman, D. J. PY - 1990 DA - 1990// TI - Basic local alignment search tool JO - J Mol Biol VL - 215 UR - https://doi.org/10.1016/S0022-2836(05)80360-2 DO - 10.1016/S0022-2836(05)80360-2 ID - Altschul1990 ER - TY - JOUR AU - Mitra, A. AU - Skrzypczak, M. AU - Ginalski, K. AU - Rowicka, M. PY - 2015 DA - 2015// TI - Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0120520 DO - 10.1371/journal.pone.0120520 ID - Mitra2015 ER - TY - JOUR AU - Camacho, C. AU - Coulouris, G. AU - Avagyan, V. AU - Ma, N. AU - Papadopoulos, J. AU - Bealer, K. AU - Madden, T. L. PY - 2009 DA - 2009// TI - BLAST+: architecture and applications JO - BMC Bioinformatics VL - 10 UR - https://doi.org/10.1186/1471-2105-10-421 DO - 10.1186/1471-2105-10-421 ID - Camacho2009 ER - TY - JOUR AU - Punta, M. AU - Coggill, P. C. AU - Eberhardt, R. Y. AU - Mistry, J. AU - Tate, J. AU - Boursnell, C. AU - Pang, N. AU - Forslund, K. AU - Ceric, G. AU - Clements, J. AU - Heger, A. PY - 2011 DA - 2011// TI - The Pfam protein families database JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1065 DO - 10.1093/nar/gkr1065 ID - Punta2011 ER - TY - JOUR AU - Petersen, T. N. AU - Brunak, S. AU - Heijne, G. AU - Nielsen, H. PY - 2011 DA - 2011// TI - SignalP 4.0: discriminating signal peptides from transmembrane regions JO - Nat Methods VL - 8 UR - https://doi.org/10.1038/nmeth.1701 DO - 10.1038/nmeth.1701 ID - Petersen2011 ER - TY - JOUR AU - Krogh, A. AU - Larsson, B. AU - Heijne, G. AU - Sonnhammer, E. L. PY - 2001 DA - 2001// TI - Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes JO - J Mol Biol VL - 305 UR - https://doi.org/10.1006/jmbi.2000.4315 DO - 10.1006/jmbi.2000.4315 ID - Krogh2001 ER - TY - JOUR AU - Lagesen, K. AU - Hallin, P. F. AU - Rødland, E. AU - Stærfeldt, H. H. AU - Rognes, T. AU - Ussery, D. W. PY - 2007 DA - 2007// TI - RNammer: consistent annotation of rRNA genes in genomic sequences JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkm160 DO - 10.1093/nar/gkm160 ID - Lagesen2007 ER - TY - JOUR AU - Powell, S. AU - Szklarczyk, D. AU - Trachana, K. AU - Roth, A. AU - Kuhn, M. AU - Muller, J. AU - Arnold, R. AU - Rattei, T. AU - Letunic, I. AU - Doerks, T. AU - Jensen, L. J. PY - 2011 DA - 2011// TI - eggNOG v3. 0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr1060 DO - 10.1093/nar/gkr1060 ID - Powell2011 ER - TY - JOUR AU - Kanehisa, M. AU - Goto, S. AU - Sato, Y. AU - Furumichi, M. AU - Tanabe, M. PY - 2011 DA - 2011// TI - KEGG for integration and interpretation of large-scale molecular data sets JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr988 DO - 10.1093/nar/gkr988 ID - Kanehisa2011 ER - TY - JOUR AU - Emms, D. M. AU - Kelly, S. PY - 2015 DA - 2015// TI - OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0721-2 DO - 10.1186/s13059-015-0721-2 ID - Emms2015 ER - TY - JOUR AU - Wang, Y. AU - Coleman-Derr, D. AU - Chen, G. AU - Gu, Y. Q. PY - 2015 DA - 2015// TI - OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv487 DO - 10.1093/nar/gkv487 ID - Wang2015 ER - TY - JOUR AU - Ekseth, O. K. AU - Kuiper, M. AU - Mironov, V. PY - 2013 DA - 2013// TI - orthAgogue: an agile tool for the rapid prediction of orthology relations JO - Bioinformatics. VL - 30 UR - https://doi.org/10.1093/bioinformatics/btt582 DO - 10.1093/bioinformatics/btt582 ID - Ekseth2013 ER - TY - JOUR AU - Cole, T. J. AU - Brewer, M. S. PY - 2018 DA - 2018// TI - FUSTr: a tool to find gene families under selection in transcriptomes JO - PeerJ. VL - 6 UR - https://doi.org/10.7717/peerj.4234 DO - 10.7717/peerj.4234 ID - Cole2018 ER - TY - JOUR AU - Miele, V. AU - Penel, S. AU - Duret, L. PY - 2011 DA - 2011// TI - Ultra-fast sequence clustering from similarity networks with SiLiX JO - BMC Bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-116 DO - 10.1186/1471-2105-12-116 ID - Miele2011 ER - TY - JOUR AU - Katoh, K. AU - Standley, D. M. PY - 2013 DA - 2013// TI - MAFFT multiple sequence alignment software version 7: improvements in performance and usability JO - Mol Biol Evol VL - 30 UR - https://doi.org/10.1093/molbev/mst010 DO - 10.1093/molbev/mst010 ID - Katoh2013 ER - TY - JOUR AU - Price, M. N. AU - Dehal, P. S. AU - Arkin, A. P. PY - 2009 DA - 2009// TI - FastTree: computing large minimum evolution trees with profiles instead of a distance matrix JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msp077 DO - 10.1093/molbev/msp077 ID - Price2009 ER - TY - JOUR AU - Yang, Z. PY - 2007 DA - 2007// TI - PAML 4: phylogenetic analysis by maximum likelihood JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm088 DO - 10.1093/molbev/msm088 ID - Yang2007 ER - TY - JOUR AU - Suyama, M. AU - Torrents, D. AU - Bork, P. PY - 2006 DA - 2006// TI - PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl315 DO - 10.1093/nar/gkl315 ID - Suyama2006 ER - TY - BOOK AU - Kück, P. PY - 2009 DA - 2009// TI - ALICUT: a Perlscript which cuts ALISCORE identified RSS. Bonn version: Department of Bioinformatics, Zoologisches Forschungsmuseum A. Koenig (ZFMK) ID - Kück2009 ER -